We investigated metric and nonmetric characteristics on 140,122 and 63 crania of Amami, Okinawa and Sakishima Islandesrs. Results of facial flatness measurements revealed the crania of Okinawa Islandesrs had very flat faces comparable to those of immigrant Yayoi and Kofun people. In this respect, not as usually considered, Okinawans are very different from Ainus and Jomons whoes facial skeletons show prominent configuration, Moreover, the incidence pattern of nonmetric cranial traits was quite different between Okinawans and Ainus or Jomons. From these results we asserted the hypothesis of close affinity between Okinawans and Ainus to be carefully reconsidered.